[Bioperl-l] From PDB to get nucleotide sequences for all related genomes?

"최상철" goshng at naver.com
Tue Oct 12 10:06:16 EDT 2004

Dear Bioperl Guru: 

I'm Sang Chul Choi, a graduate student in the program of bioinformatics at NCSU. 
I'm interested in Protein Evolution Modeling and recently I should apply a 
model to all PDB entries. The problem is that I am stuck in getting nucleotide 
sequences of all related genomes for each PDB entry. 

There is "DBREF" section in PDB like this: 
DBREF 1T7S A 74 210 GB 17507755 NP_491893 74 210 
DBREF 1T7S B 74 210 GB 17507755 NP_491893 74 210 
DBREF 1T9F A 22 206 GB 17508635 NP_491320 22 206 
DBREF 1TC3 A 1 21 PDB 1TC3 1TC3 1 21 
DBREF 1TC3 B 101 120 PDB 1TC3 1TC3 101 120 
DBREF 1TC3 C 202 252 GB 1086778 P34257 2 52 

And, I know that there is the source orgarnism section. 

Using these two kinds of information, I have tried to get nucleotide sequences 
from Database: NCBI, SWISSPROT, ... 

Is there any good suggestion for this thing? Any comment will be helpful. 


Sang Chul 

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